Uses of Interface
org.biopax.paxtools.pattern.miner.SIFMiner

Packages that use SIFMiner

Package	Description
org.biopax.paxtools.pattern.miner	Package for pattern miner utility.

Uses of SIFMiner in org.biopax.paxtools.pattern.miner

Classes in org.biopax.paxtools.pattern.miner that implement SIFMiner

Modifier and Type	Class	Description
class	AbstractSIFMiner	Base class for SIF Miners.
class	CatalysisPrecedesMiner	Miner for the catalysis-precedes pattern.
class	ChemicalAffectsThroughBindingMiner	Miner for the chemical-affects-protein pattern.
class	ChemicalAffectsThroughControlMiner	Miner for the chemical-affects-protein pattern.
class	ConsumptionControlledByMiner	Miner for the consumption-controlled-by pattern.
class	ControlsDegradationIndirectMiner	Yet another miner for the controls-degradation pattern.
class	ControlsExpressionMiner	Miner for the transcriptional regulation pattern.
class	ControlsExpressionWithConvMiner	Miner for the transcriptional regulation pattern, modeled using Conversion.
class	ControlsPhosphorylationMiner	Miner for the controls-phosphorylation pattern.
class	ControlsProductionOfMiner	Miner for the controls-production-of pattern.
class	ControlsStateChangeOfMiner	Miner for the controls-state-change pattern.
class	ControlsTransportMiner	Miner for the controls-transport pattern.
class	ControlsTransportOfChemicalMiner	Miner for the controls-transport-of-chemical pattern.
class	CSCOBothControllerAndParticipantMiner	Miner for the controls-state-change pattern.
class	CSCOButIsParticipantMiner	Miner for the controls-state-change pattern.
class	CSCOThroughBindingSmallMoleculeMiner	Miner for the controls-state-change pattern.
class	CSCOThroughControllingSmallMoleculeMiner	Miner for the controls-state-change pattern.
class	CSCOThroughDegradationMiner	Miner for the degradation pattern.
class	InComplexWithMiner	Miner for the degradation pattern.
class	InteractsWithMiner	Miner for the "interacts-with" relation.
class	NeighborOfMiner	Miner for the "neighbor-of" relation.
class	ReactsWithMiner	Miner for the "reacts-with" relation.
class	UsedToProduceMiner	Miner for the "used-for-production-of" relation.

Methods in org.biopax.paxtools.pattern.miner that return types with arguments of type SIFMiner

Modifier and Type	Method	Description
List<Class<? extends SIFMiner>>	SIFEnum.getMiners()
List<Class<? extends SIFMiner>>	SIFType.getMiners()	Gets the list of SIFMiner classes that can search this type of SIF edge in a BioPAX model.

Constructors in org.biopax.paxtools.pattern.miner with parameters of type SIFMiner

Modifier	Constructor	Description
	SIFSearcher(IDFetcher idFetcher, SIFMiner... miners)	Constructor with ID fetcher and miners.
	SIFSearcher(SIFMiner... miners)	Constructor with miners.